Cycles bake with separate uv maps?
See my answer here:


  A screenshot just to show how things are initially:
  
  
  
  
  Create a new UV map in Properties > Object data, then with it selected, edit or re-unwrap to make the second UV map layed out how
  you want it:
  


In your case, Lightmap pack or Smart UV unwrap will probably do fine for the unwrap method.


  
  
  
  Create a new image to bake to by pressing &#9095; AltN in the image editor, or by pressing new in
  header > Image:
  
  
  Add a texture node to your material(s), set to the image you want to bake to.
  


Here set the bake type as combined, then select the texture node and press bake:




  After it's baked, remember to save the image. F3 to save it
  to disk, or header > image > Pack as PNG to pack it into the .blend
  as a png.